Lactobacillus nasalidis sp. nov., isolated from the forestomach of a captive proboscis monkey (Nasalis larvatus)

References

1. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article][PubMed]
   [Google Scholar]
2. Duar RM, Lin XB, Zheng J, Martino ME, Grenier T et al. Lifestyles in transition: evolution and natural history of the genus Lactobacillus . FEMS Microbiol Rev 2017; 41:S27–S48 [View Article][PubMed]
   [Google Scholar]
3. Zheng J, Wittouck S, Salvetti E, Franz CM, Harris HM et al. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae . Int J Syst Evol Microbiol 2020; 70:2782–2858 [View Article][PubMed]
   [Google Scholar]
4. Endo A, Futagawa-Endo Y, Dicks LMT. Diversity of Lactobacillus and Bifidobacterium in feces of herbivores, omnivores and carnivores. Anaerobe 2010; 16:590–596 [View Article][PubMed]
   [Google Scholar]
5. Tsuchida S, Kitahara M, Nguema PPM, Norimitsu S, Fujita S et al. Lactobacillus gorillae sp. nov., isolated from the faeces of captive and wild western lowland gorillas (Gorilla gorilla gorilla). Int J Syst Evol Microbiol 2014; 64:4001–4006 [View Article][PubMed]
   [Google Scholar]
6. Tsuchida S, Murata K, Ohkuma M, Ushida K. Isolation of Streptococcus gallolyticus with very high degradability of condensed tannins from feces of the wild Japanese rock ptarmigans on Mt. Tateyama. J Gen Appl Microbiol 2017; 63:195–198 [View Article][PubMed]
   [Google Scholar]
7. Matsuda I, Murai T, Clauss M, Yamada T, Tuuga A et al. Regurgitation and remastication in the foregut-fermenting proboscis monkey (Nasalis larvatus). Biol Lett 2011; 7:786–789 [View Article][PubMed]
   [Google Scholar]
8. Hayakawa T, Nathan S, Stark DJ, Saldivar DAR, Sipangkui R et al. First report of foregut microbial community in proboscis monkeys: are diverse forests a reservoir for diverse microbiomes?. Environ Microbiol Rep 2018; 10:655–662 [View Article][PubMed]
   [Google Scholar]
9. Tsukahara T, Ushida K. Succinate accumulation in pig large intestine during antibiotic-associated diarrhea and the constitution of succinate-producing flora. J Gen Appl Microbiol 2002; 48:143–154 [View Article][PubMed]
   [Google Scholar]
10. Naser SM, Thompson FL, Hoste B, Gevers D, Dawyndt P et al. Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology 2005; 151:2141–2150 [View Article][PubMed]
    [Google Scholar]
11. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
12. Jukes TH, Cantor CR. Evolution of protein molecules. Mammalian protein metabolism 1969; 3:21–132
    [Google Scholar]
13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
14. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
15. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
16. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article][PubMed]
    [Google Scholar]
17. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. mega X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
    [Google Scholar]
18. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][PubMed]
    [Google Scholar]
19. Kajitani R, Yoshimura D, Ogura Y, Gotoh Y, Hayashi T et al. Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process. DNA Res 2020; 27:dsaa014 [View Article][PubMed]
    [Google Scholar]
20. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:1–10 [View Article]
    [Google Scholar]
21. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
    [Google Scholar]
22. Katayama-Fujimura Y, Komatsu Y, Kuraishi H, Kaneko T. Estimation of DNA base composition by high performance liquid chromatography of its nuclease Pi hydrolysate. Agric Biol Chem 1984; 48:3169–3172 [View Article]
    [Google Scholar]
23. Barrow GI, Feltham RKA. (editors) Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press; 1993
    [Google Scholar]
24. Kawamoto I, Oka T, Nara T. Cell wall composition of Micromonospora olivoasterospora, Micromonospora sagamiensis, and related organisms. J Bacterol 1981; 146:527–534 [View Article][PubMed]
    [Google Scholar]
25. Ahmed I, Kudo T, Abbas S, Ehsan M, Iino T, Fujiwara T et al. Cellulomonas pakistanensis sp. nov., a moderately halotolerant Actinobacteria. Int J Syst Evol Microbiol 2014; 64:2305–2311 [View Article][PubMed]
    [Google Scholar]
26. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
27. Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC. Whole-genome prokaryotic phylogeny. Bioinformatics 2005; 21:2329–2335 [View Article][PubMed]
    [Google Scholar]
28. Kudo Y, Oki K, Watanabe K. Lactobacillus delbrueckii subsp. sunkii subsp. nov., isolated from sunki, a traditional Japanese pickle. Int J Syst Evol Microbiol 2012; 62:2643–2649 [View Article][PubMed]
    [Google Scholar]
29. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article][PubMed]
    [Google Scholar]
30. Unwin S, Ancrenaz M, Handling BW. Anaesthesia, health evaluation and biological sampling. In Setchell J, Curtis D. (editors) Field and Laboratory Methods in Primatology: A Practical Guide Cambridge: Cambridge University Press; 2011 pp 147–168
    [Google Scholar]
31. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article][PubMed]
    [Google Scholar]
32. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article][PubMed]
    [Google Scholar]
33. Kim JS, Choe H, Kim KM, Lee YR, Rhee MS et al. Lactobacillus porci sp. nov., isolated from small intestine of a swine. Int J Syst Evol Microbiol 2018; 68:3118–3124 [View Article][PubMed]
    [Google Scholar]